President-elect Uhuru Kenyatta greets his supporters in the company of his wife, Margaret, soon after attending a church service in his rural hometown of Gatundu, north of the capital, Nairobi, March 10.

But Kenya is one of the West’s most important allies in sub-Saharan Africa, a stalwart in the fight against militant Islam, and a regional powerhouse hosting international investors, aid agencies, and more than a million tourists a year.

“It’s going to be very complicated,” says Gladwell Otieno, a leading Kenyan rights campaigner and director of the Africa Center for Open Governance. “Kenya’s partners have spelled out their positions on ICC indictees, but at the same time their relationship with us is so close and so important, especially on questions of security and antiterror, that they are truly in a dilemma.”

ICC prosecutors have charged Mr. Kenyatta with five counts of crimes against humanity that include “indirect co-perpetration” of murder, rape, and persecution, over his alleged involvement in aspects of the violence that followed Kenya’s 2007 election.

His deputy president, William Ruto, separately faces three similar counts.

Both men deny the charges and have repeatedly pledged to cooperate with the court’s proceedings.

Western power warnings

Despite this, the pair’s Jubilee Alliance coalition has repeatedly painted the trials as assaults on Kenya’s sovereignty, even going so far as to suggest last week's elections were a referendum on the court’s right to investigate Kenya’s affairs.

This nationalistic rhetoric gathered more force when the US, Britain, and the European Union said before the polls that their policy would not allow them to meet with anyone indicted at the ICC apart unless it was for “essential” matters.

Johnnie Carson, President Obama’s assistant secretary of State for African Affairs, drew sharp criticism from many in Kenyatta’s camp for stating that Kenyan voters’ choice at the ballots would have “consequences.”

It is widely accepted that these statements were interpreted in Kenya as a warning not to vote for Kenyatta, and that they backfired. With all the results counted, Kenyatta polled more than 6 million votes.

Election analysis suggested that a significant portion of his support base rallied strongly to his cause because they felt putting him in power would somehow shield him from prosecution.

That is not the case, and Kenyatta acknowledged as much in his acceptance speech Saturday, promising that he would “continue to cooperate with all … international institutions.”

Kenyatta's cooperation matters

Diplomats posted to Nairobi have stressed the difference between how they act toward an ICC indictee who cooperates with the court, and one who does not.

If Kenyatta and Mr. Ruto renege on their promises and fail to turn up for their trials, a far more serious tranche of actions are triggered, including arrest warrants, individual sanctions, and potentially global financial isolation.

There is likely to be some pragmatism in the application of supposedly red-line international protocols toward Kenya, says Mwalimu Mati, head of Mars Group Kenya, a domestic anticorruption watchdog.

“There is a good deal of self-confidence in the Kenyatta camp that Kenya is too big to fail,” he says.

Comparisons to Sudan, where President Omar al-Bashir has been hit with travel bans and sanctions for ignoring ICC charges, are misplaced in the Kenyan context, he continues.

“Kenyans see their country at a different level to other African nations. They expect hard and fast rules never to be insisted upon because Kenya has a special relationship to the West that, while troubled, will always be permanent.”

Remote governing

Aside from how Kenyatta will conduct business with important allies who will not talk to him, his trial at The Hague will also force him and his deputy to spend long periods of time away from Kenya.

Fatou Bensouda, the ICC prosecutor, has said she has more than 800 hours of evidence to present against Kenyatta, and 500 hours against Ruto.

It is unlikely that either case will conclude for several years, and activists and Kenyatta’s main election rival, Raila Odinga, have questioned how they can run the country when they will so often be absent.

Cabinet meetings will take place without them, military operations must be planned while they are away (Kenyan troops are battling Al Shabab in Somalia), and parliamentary bills will go unsigned potentially for weeks.

“The fact of being accused persons places practical limitations on their lives, which in turn make it impractical that they can run a country,” a coalition of Kenyan rights groups and lawyers said in a preelection report.

In comments before the elections, Kenyatta dismissed this, saying that if Kenyans voted him into power, they were confirming that they trusted him both to appear at The Hague and to manage his country's affairs.

"There’s nothing to prevent the two processes from moving side by side," he said in a television interview last week.